Time Machine does not backup deleted files. The whole point of maintaining a backup is to make copies before files are deleted -- so that if you want to restore them after deletion, you can do so.
It is not useful to think of deleted files as merely 'marked for deletion but still there'.
Having said that, the APFS format does make 'local snapshots', ...
No. Time Machine only backs up files present on the filesystem and furthermore, only those not excluded by a rule or explicit exception.
On OS X, what files are excluded by rule from a Time Machine backup?
What does Time Machine back up?
Deleting a lot of files from Trash via Finder/Empty Trash can be very slow sometimes. It might be easier/faster to run
rm -r ~/.Trash
in Terminal (at least it won't partially block the UI while doing so).
PS: If the files to be deleted are on an external drive you need to delete them from /Volumes/VOLNAME/.Trash instead.
When I try to use "ls" cmd in the terminal, it also takes over 10 mins and does not display anything.
This is not normal. Something is amiss. I'd see the most likely cause as either a bad filesystem or a failing drive. While surprising, it could be a bad spot on the drive just where the directory is. In the case of a failing drive, macOS will try multiple ...